Previously it has been shown that the floral scent of snapdragon flowers consists of a relatively simple mixture of volatile organic compounds (VOCs). These compounds are thought to be involved in the attraction of pollinators; however, little is known about their effect on other organisms, such as neighboring plants. Here, we report that VOCs from snapdragon flowers inhibit Arabidopsis root growth. Out of the three major snapdragon floral volatiles, myrcene, (E)-beta-ocimene, and methyl benzoate (MB), MB was found to be primarily responsible for the inhibition of root growth. Ten micromoles MB reduced root length by 72.6%. We employed a microarray approach to identify the MB target genes in Arabidopsis that were responsible for the root growth inhibition phenotype in response to MB. These analyses showed that MB treatment affected 1.33% of global gene expression, including cytokinin, auxin and other plant-hormone-related genes, and genes related to seed germination processes in Arabidopsis. Accordingly, the root growth of cytokinin (cre1) and auxin (axr1) response mutants was less affected than that of the wild type by the volatile compound: roots of the treated mutants were reduced by 45.1 and 56.2%, respectively, relative to untreated control mutants.